[ccp4bb] How to generate a complete viirus PDB
Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
Re: [ccp4bb] How to generate a complete viirus PDB
Hi Hong, you can usually download the 'biological assembly' from the PDBe, be warned that for viruses this is rather large, cheers, Matt. On 25/04/2013 08:19, Guan Hong Hsiang wrote: Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===
Re: [ccp4bb] How to generate a complete viirus PDB
Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guan Hong Hsiang Sent: Wednesday, April 24, 2013 11:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to generate a complete viirus PDB Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
Re: [ccp4bb] How to generate a complete viirus PDB
Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one : http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdband then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney bmkea...@ncsu.edu wrote: Hi Hong, ** ** I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool ( http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. ** ** Brad ** ** --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Guan Hong Hsiang *Sent:* Wednesday, April 24, 2013 11:19 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] How to generate a complete viirus PDB ** ** Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
Re: [ccp4bb] How to generate a complete viirus PDB
Hi Hong, In your PDB file if the BIOMT transformation matrix (under remark 350) is provided, you can use this script to generate the biological assembly : http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ Greetings, Abhi On Thu, Apr 25, 2013 at 9:31 AM, sujata halder halder.suj...@gmail.comwrote: Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one : http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdband then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney bmkea...@ncsu.eduwrote: Hi Hong, ** ** I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool ( http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. ** ** Brad ** ** --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Guan Hong Hsiang *Sent:* Wednesday, April 24, 2013 11:19 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] How to generate a complete viirus PDB ** ** Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang -- *Abhimanyu Kumar Singh *Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.es
[ccp4bb] ECM Meeting in Warwick, 25th-29th August
Just a reminder to register for this year's European Crystallography Meeting at the University of Warwick, being held from 25th-29th August. Early bird registration is only available until the 6th May. In addition to the main meeting, The European Young Crystallographers satellite meeting will take place on Sunday 25th August, prior to the ECM opening ceremony. This satellite meeting will be the first of its kind at a European level and will run from 9.00 am to 5.00 pm. The opening lecture will be a plenary by Dr Birger Dittrich, followed by three sessions for oral presentations and a poster session dedicated to young crystallographers (anyone under the age of 35) presenting their work. This is a great opportunity for younger researchers to present in a more relaxed environment and to network with others. The satellite meeting will cost £15 to attend, and this includes registration, coffee and lunch. This fee has been subsidized by the European Crystallographic Association and the International Union of Crystallography, and we are very grateful for their financial support. Registration for both the ECM and satellite meeting can be done on the ECM28 website: http://ecm28.ecanews.org/registration/ We look forward to seeing you all in Warwick! Dr Anna Warren Postdoctoral Research Associate, I24 Microfocus Macromolecular Crystallography Beamline http://www.diamond.ac.uk/I24 Diamond Light Source anna.war...@diamond.ac.ukmailto:anna.war...@diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] How to generate a complete viirus PDB
Hi all, There's also a tool available for converting PDB files into the viper format available at http://viperdb.scripps.edu/pdbToViper.php Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: sujata halder [mailto:halder.suj...@gmail.com] Sent: Thursday, April 25, 2013 12:32 AM To: Bradley Kearney Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How to generate a complete viirus PDB Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one :http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdband then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney bmkea...@ncsu.edu wrote: Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guan Hong Hsiang Sent: Wednesday, April 24, 2013 11:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to generate a complete viirus PDB Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
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Re: [ccp4bb] How to generate a complete viirus PDB
Would PISA not do this? -- Eugene On 25 Apr 2013, at 09:20, abhimanyu singh wrote: Hi Hong, In your PDB file if the BIOMT transformation matrix (under remark 350) is provided, you can use this script to generate the biological assembly : http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ Greetings, Abhi On Thu, Apr 25, 2013 at 9:31 AM, sujata halder halder.suj...@gmail.commailto:halder.suj...@gmail.com wrote: Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one :http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdband then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney bmkea...@ncsu.edumailto:bmkea...@ncsu.edu wrote: Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.eduhttp://viperdb.scripps.edu/. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guan Hong Hsiang Sent: Wednesday, April 24, 2013 11:19 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to generate a complete viirus PDB Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang -- Abhimanyu Kumar Singh Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.esmailto:abhimanyu.si...@cnb.csic.es -- Scanned by iCritical.
Re: [ccp4bb] How to generate a complete viirus PDB
Dear Hong, As Eugene mentioned, you should be able to build the full virus assembly using PISA. Another option is to use the multiscale model menu of UCSF Chimera (default setting is Biological Assembly) to generate the complete virus assembly from PDB BIOMT records. If this is a new structure any you have only ncs records to build the crystal asymmetric unit, you can still use Chimera/multiscale model with option to apply both NCS and crystal symmetry. Cathy Lawson EM Project Manager, RCSB-PDB
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Re: [ccp4bb] salt or not?
Careina, One thing to try if other ideas don't work or are too difficult, is covalently (therefore unambiguously) labelling a little of your protein with a fluorescent dye. If you add 20 nL of this to the drop *after the crystals have grown*, protein crystals will light up, but salt crystals will not. Thermo make some very easy-to-use kits for labelling. See methods section of our paper *Cryst. Growth Des.*, 2011, *11* (8), pp 3432–3441. Could you also label the DNA . . . ? Hope it helps, best wishes, Patrick On 15 April 2013 11:18, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear ccp4 I have been performing trials on a protein DNA complex for a while now and have not seen any crystals form. Today I checked an old plate (over a month old) and I see 4 large crystals. *excitement* Three of them look tetragonal in shape (like a pyramid) and one of them looks hexagonal. I do not know if they are salt or protein. There is calcium chloride in the buffer. They feel quite soft to touch. They do not cause much birefringence. One of them does not seem to absorb much izit. It did go a bit blue but not entirely. How can I tell if this crystal is protein or not? Do you think its worth trying to see how it diffracts? Also, does Izit affect diffraction/ protein structures at all? Could I use a crystal with Izit in a diffraction experiment and ultimately to get the structure? Best Careina -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] Curious electron density associated with Asp sidechain
Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. I have tried a number of different modelling scenarios, but as yet can't reach a wholly satisfactory conclusion; waters, alternate conformers, really don't seem to cut it. I though about some radiation-induced phenomena, but this data set was collected on a home-source, so I guess this is unlikely. So, I would really appreciate some ideas and suggestions. Hopefully it is blindingly obvious to someone. Random Thought: could it be PEGylation of the side-chain? Some other hopefully useful background information: * I'm sure it is/was an ASP, because the same protein (made from the same construct) has been used in previous crystallisations, and the resultant structures have clear, unambiguous electron density for the side chain. * the crystallization condition is PEG 200, with some Na/K phosphate at pH 5.8, and NaCl. The protein itself contains HEPES buffer. With many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
Re: [ccp4bb] Curious electron density associated with Asp sidechain
Call EBI, consider some kind of chemical modification. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 25, 2013, at 19:10 , Antony Oliver antony.oli...@sussex.ac.uk wrote: Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. I have tried a number of different modelling scenarios, but as yet can't reach a wholly satisfactory conclusion; waters, alternate conformers, really don't seem to cut it. I though about some radiation-induced phenomena, but this data set was collected on a home-source, so I guess this is unlikely. So, I would really appreciate some ideas and suggestions. Hopefully it is blindingly obvious to someone. Random Thought: could it be PEGylation of the side-chain? Some other hopefully useful background information: * I'm sure it is/was an ASP, because the same protein (made from the same construct) has been used in previous crystallisations, and the resultant structures have clear, unambiguous electron density for the side chain. * the crystallization condition is PEG 200, with some Na/K phosphate at pH 5.8, and NaCl. The protein itself contains HEPES buffer. With many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
[ccp4bb] Factor 10a protease
Dear colleagues, i hope every one doing well. i am trying to remove the 10x his tag , as i tried to crystallize with the tag but i didn^t obtain crystals unless some salt crystals , very small crystals and some precipitant. i want to use factor 10a protease but i didn^t tried it before. this is the first time for using it. i have factor 10a protease from Qiagen 400 unit . i have read the protocol but i still need some suggestion and experience as you know it is expensive. also i have another question , how many protein digested by one unit ? i know it depend but roughly how much? i really appreciate your support. best regards Amr
Re: [ccp4bb] Curious electron density associated with Asp sidechain
Hello Tony is that Asp-Gly? If so, it could be prone to succinimide formation. Check out this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323960/ and references therein! Good luck Jon.Cooper --- On Thu, 25/4/13, Antony Oliver antony.oli...@sussex.ac.uk wrote: From: Antony Oliver antony.oli...@sussex.ac.uk Subject: [ccp4bb] Curious electron density associated with Asp sidechain To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 25 April, 2013, 17:10 Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. I have tried a number of different modelling scenarios, but as yet can't reach a wholly satisfactory conclusion; waters, alternate conformers, really don't seem to cut it. I though about some radiation-induced phenomena, but this data set was collected on a home-source, so I guess this is unlikely. So, I would really appreciate some ideas and suggestions. Hopefully it is blindingly obvious to someone. Random Thought: could it be PEGylation of the side-chain? Some other hopefully useful background information: * I'm sure it is/was an ASP, because the same protein (made from the same construct) has been used in previous crystallisations, and the resultant structures have clear, unambiguous electron density for the side chain. * the crystallization condition is PEG 200, with some Na/K phosphate at pH 5.8, and NaCl. The protein itself contains HEPES buffer. With many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
